I’m currently merging several PIs’ publication lists into one document for a grant progress report. I’m sorting by year of publication and then alphabetically by first author. It’s really, really fun, although actually not the absolute worst thing to do on a Friday afternoon.
There’s a bit of a tight character limit, and I’m wearing out my backspace key on all the completely unnecessary fluff that some citation formats use. I just need the full author list, title, journal, volume and page numbers, and year. So why do so many formats introduce the following?
- unnecessary punctuation marks. Author name and date should be “Ennis CA, 2009” rather than “Ennis, C. A., (2009)” and all possible permutations and combinations of intermediate punctuation.
- unnecessary use of “and” in author lists. Just put a comma before the last author. Those two extra spaces really add up.
- full journal names. We all know what the abbreviations mean. And don’t put spaces between the individual letters of acronyms (it’s USA, not U S A).
- journal issue number. I would bet good money that most people find articles online by author, volume and page, rather than by hunting down individual print issues. I don’t need to turn 24:345-9 into 24(11):345-9. And what’s with all the additional numbers and spaces? (24: (11); 345 – 349, you can bugger right off).
- month and day of publication. I just need the year.
- doi or PubMed ID in citations that already have the volume and page number. WHY??!!
This is what happens when people prepare their CVs using different Endnote output styles1. (I’m assuming the typos and duplicated years in some citations are due to human error rather than software glitches). I don’t have access to the original Endnote libraries, so I’m in Word, using find and replace wherever possible, and doing the rest manually.
The attempt to create more space is proceeding slooooooowly. What a waste of time.
/rant.
1 Let’s not even get into the different order of the citation components, and different italics / bold / underlining conventions.
This is what happens when people prepare their CVs using different Endnote output styles
Hmmm, so it’s possible that there is indeed a positive aspect to having an institutional electronic CV with a standard citation format.
Believe it or not, it may be true.
BTW anyone who wants to read something more cheerful and/or cheer me up should comment on this post. Or bring me some chocolate.
I should point out that actually drafting the progress report was kinda fun.
Cath – I do way too much of this (I suspect for many of the same granting agencies you do). My general solution is to pull all the relevant publications from PubMed using a logical query – all the PI names and the appropriate date range restriction, then dump the PubMed output to text and massage it from there.
You still have to f*rt around getting rid of all the spurious carriage returns PubMed’s text output introduces, but at least all the papers are in the same format.
Faced with a bunch of hardcopy CVs and no way to search in one fell swoop, I might still search each publication separately and paste the resulting text citation into a list. At least then I can follow the same process for fixing each citation (rather than using a different set of backspaces/replacements/whatever for each separate CV’s worth).
Of course, one might argue that the Common CV format should take care of this, but of course it doesn’t.
What would be nice would be a little applet like what the NN profile does – put in a PMID and it spits out a nicely formatted citation in a consistent format. If it were programmable, it would be excellent.
Hm…
Hmmm, that would be nice.
I like the PubMed idea – but it would be pretty damn difficult for this particular project. I’m using only a subset of each PI’s papers (the ones that use a particular grant-funded core platform), and need each PI to identify exactly which of their papers qualify. So they’re cutting and pasting from their CVs, and sending the citations to me in Word or in the body of the email.
It’s done now, for those citations that I actually have anyway! Kyrsten is, once again, coming to my rescue and inviting me to the pub. My
sneaking out down the back stairsperfectly legitimate departure is imminent.Cath, I actually like to have the doi in the citation. It’s the easiest way to uniquely identify a paper and to get the fulltext PDF.
Our university requires us to put all our published papers into a central RefWorks database. For the very reason to make it easier to create these kinds of lists.
Cath – if you have your PI’s CVs in a word document (with publications entered by Endnote), could you not re-format these with your preferred style (customised to your liking if need be)?
Or, better still, from these documents, export the travelling Endnote libraries, merge these into one library and get Endnote to do the chronological sorting for you?
Martin, I agree that it’s useful, but it just takes up too much space in this format!
I really like the idea of these centralised databases. We don’t have anything like that, maybe I should suggest it.
Stephen, I tried to do that, but it actually turned out that only a couple of PIs had sent me anything I could extract Endnote citations from. The high incidence of typos within the references made me suspect that they’d been typed in manually rather than put in using Endnote. A lot of the others were pasted from PubMed, with hyperlinks and all kinds of other crap embedded. A very messy project, which is now thankfully finished!
BTW Richard, putting dois or PIDs into the common CV would be an awesome way to do this – that way the CV system itself could decide which papers to include in a given formatted CV (different agencies having different year ranges and ordering conventions). But sadly there’s just the field for the number of papers, and then each agency has its own way for you to spend hours putting the references in manually.
You make it sound like all I do is ask you to the pub. But I suspect you had a great time with all the geeky scientists (and those that have perhaps smartly, changed careers). We need more afternoons like that – they help keep the craziness in perspective.
Pub nights with scientific content – does that sound better?!
Oh, what fresh level of hell is this?
From the instructions: “List all publications, published, in press or submitted for publication, specifically resulting from the research conducted under this grant since it was awarded two and half years ago. Additional pages may be added. Please provide a copy of these publications.” (emphasis mine).
Did I mention that this is a grant for a core platform? That is used by multiple PIs? There are at least 54 publications.
Sigh. Cath dons
a suit of armouriPod earbuds and prepares for an afternoon ofbattling dragonsfinding and saving PDFs.now I’m on the dark side I too spend hours performing menial, pointless chores like this. Good chance to catch up with Podcasts…
That’s exactly what I’m doing. After the initial shock of hearing exactly how loud I’d had to turn the volume up to hear the podcast over the background noises on the bus this morning, I’m enjoying the soothing tones of Stephen Fry.
I too spend hours performing menial, pointless chores like this.
Two words: “undergraduate interns”.
(cough)
That’s a great idea Jenny. Unfortunately, the Powers That Be are not convinced.
Part of the problem is that, at least in my job, these things tend to crop up without much warning. For the rest of the time, there would be little for an undergrad to actually do. Proofreading of whatever I’m working on, I suppose, or summarising particular papers. Although even then I would feel the need to check it myself anyway (must… suppress… control freak tendencies…)
Incidentally, determined to make the best of things, I’ve found some small amusement from today’s task. A first author on a couple of these papers has a first name beginning with F and a middle name beginning with M, making her sound, in citation format, like a radio station.
This pleases me.
Incidentally, I’m sorry to have nixed so many of the excellent suggestions that people have made in this thread. I hate to be so negative, but they wouldn’t have helped me in this particular task, which needed to be done in the fastest possible way in the short term, without considering better ways to do it in the future. I’m trying to figure out the best ways to implement some of these ideas in the long term. Thanks again everyone!